Statistical Thermodynamics and Molecular Simulation aim at describing the properties of systems that consist of many individual particles (atoms, molecules). Although the properties of the complete system follow directly from the properties and interactions of the individual particles, usually these properties cannot be calculated directly by using pen and paper only. Computer simulations are a convenient and modern tool to actually calculate these properties. These so-called molecular simulations are widely used in the field of chemistry and physics to (1) predict properties of existing or new materials, (2) predict new phenomena, which may lead to new experiments and the development of new theories (3) test approximate theories for these systems. Our book is organized into two parts. In Part I, the concepts of statistical thermodynamics are illustrated with simple computer simulations. These concepts (for example the second law of thermodynamics) can be quite abstract for beginning students. Our teaching experience is that computer simulations are an excellent tool for understanding these concepts. This part of the book is specifically aimed at the bachelor level. In Part II, the basics of molecular simulations are explained based on the concepts that were introduced in Part I. It is shown how these simulations can be used to calculate properties of systems of interacting molecules. This part of the book is specifically aimed at the master level. A beginning master student with some basic knowledge of classical thermodynamics will be able to start with Part II of the book.